Showing : scrnaseq • reset
0
votes
1
reply
100
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
11 days ago • updated 5 days ago Francesco Silvestro • 0
1
vote
9
replies
731
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
21 days ago • updated 18 days ago Raya • 0
1
vote
2
replies
208
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 29 days ago by 53k • written 29 days ago by • 0
0
votes
11
replies
726
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
4 weeks ago • updated 25 days ago Peter Hickey ▴ 760
0
votes
3
replies
826
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
0
replies
272
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
6 months ago Muhammad • 0
0
votes
3
replies
754
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 7 months ago by • 0 • written 7 months ago by ▴ 10
2
votes
2
replies
745
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 12 months ago by ▴ 10
0
votes
0
replies
681
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
14 months ago Damini • 0
1
vote
8
replies
1.7k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 14 months ago by 53k • written 14 months ago by • 0
0
votes
0
replies
582
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
15 months ago Bibi • 0
0
votes
1
reply
885
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 17 months ago by ★ 4.9k • written 17 months ago by • 0
0
votes
2
replies
939
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
17 months ago rocanja ▴ 60
0
votes
1
reply
682
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 18 months ago by ★ 4.9k • written 18 months ago by • 0
1
vote
2
replies
1.9k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
21 months ago ruba-mahmoud • 0
0
votes
2
replies
1.3k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
23 months ago Momo • 0
0
votes
1
reply
782
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.1 years ago by ★ 4.9k • written 2.1 years ago by • 0
2
votes
5
replies
1.7k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.1 years ago duez.tolga • 0
0
votes
1
reply
2.7k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.1 years ago by ★ 4.9k • written 2.1 years ago by • 0
4
votes
3
replies
1.6k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
votes
1
reply
852
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 2.1 years ago by ★ 4.9k • written 2.1 years ago by • 0
0
votes
1
reply
910
views
library(topGO) query
topGO scRNAseq
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
0
votes
0
replies
719
views
adding noise to scRNA Seq counts
scRNAseq
2.2 years ago Jiyuan • 0
1
vote
11
replies
9.1k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 22 months ago by • 0 • written 2.2 years ago by • 0
2
votes
3
replies
2.0k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.3 years ago • updated 2.2 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
964
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
2.3 years ago info ▴ 10
0
votes
1
reply
1.1k
views
scRNAseq Download Errors
scRNAseq
updated 2.4 years ago by 4.2k • written 2.4 years ago by ★ 1.6k
2
votes
0
replies
2.4k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.4 years ago Tadeoye ▴ 20
0
votes
1
reply
1.4k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by ▴ 10
4
votes
5
replies
2.8k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 22 months ago by • 0 • written 2.5 years ago by • 0
0
votes
3
replies
2.2k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 14 months ago by • 0 • written 2.8 years ago by • 0
1
vote
2
replies
1.9k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.9 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.4k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
2.9 years ago evocanres • 0
0
votes
3
replies
1.7k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
2.9 years ago Madiha • 0
4
votes
5
replies
4.0k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.1 years ago Peter Hickey ▴ 760
4
votes
2
replies
1.8k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.1 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.1 years ago by ★ 29k • written 3.1 years ago by ▴ 40
0
votes
0
replies
1.4k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
3.1 years ago peter.kharchenko ▴ 30
0
votes
0
replies
1.1k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.1 years ago Sebastian Lewandowski • 0
1
vote
4
replies
1.9k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
3.1 years ago Chise ▴ 10
0
votes
0
replies
1.6k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.2 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.6k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.2 years ago by ★ 4.9k • written 3.2 years ago by • 0
0
votes
1
reply
1.7k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.2 years ago by ★ 4.9k • written 3.2 years ago by • 0
2
votes
8
replies
2.4k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.2 years ago Kelen ▴ 10
0
votes
1
reply
1.1k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
1
vote
2
replies
2.9k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.4 years ago Ismail • 0
1
vote
1
reply
2.8k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.4 years ago by ▴ 760 • written 3.4 years ago by • 0
2
votes
2
replies
2.0k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.6 years ago • updated 3.5 years ago behr201 • 0
2
votes
2
replies
1.9k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.6 years ago Hasan Alanya • 0
94 results • Page 1 of 2
Recent ...
Replies
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values by Lina ▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Votes
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Awards • All
Popular Question to Nik dAK ▴ 10
Popular Question to Michael • 0
Popular Question to sum31278 • 0
Popular Question to Gordon Smyth 53k
Popular Question to boczniak767 ▴ 740
Locations • All
San Diego, 21 minutes ago
Barcelona, Spain, 38 minutes ago
The city by the bay, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 705 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6